def add_tags(alignedSegment: pysam.AlignedSegment) -> pysam.AlignedSegment:
""" Takes an AlignedSegment and add percent identity and alignment length as tags
alignment length = MID
mismatches = NM
percent identity = (MID - NM) / MID
The percent identity is a value between 0.0 and 1.0
If the segment is unmapped then it is returned as with a percent identity of 0
and an alignment length of 0.
:param alignedSegment: The pysam AlignedSegment object
:return: alignedSegment: The updated pysam AlignedSegment object
"""
# Assuming that if the id tag is present that the other tags are also there.
if alignedSegment.has_tag('id'):
return alignedSegment
if alignedSegment.is_unmapped:
alignedSegment.set_tag('id', 0.0, 'f')
alignedSegment.set_tag('al', 0, 'i')
alignedSegment.set_tag('qc', 0.0, 'f')
return alignedSegment
alnlength = sum(alignedSegment.get_cigar_stats()[0][0:3])
query_covered_bases = sum(alignedSegment.get_cigar_stats()[0][0:2])
query_length = alignedSegment.infer_read_length()
mismatches = alignedSegment.get_tag('NM')
percid = (alnlength - mismatches) / float(alnlength)
qcov = query_covered_bases / float(query_length)
alignedSegment.set_tag('id', percid, 'f')
alignedSegment.set_tag('qc', qcov, 'f')
alignedSegment.set_tag('al', alnlength, 'i')
return alignedSegment
def from_aligned_segment(cls,
align: pysam.AlignedSegment) -> "AlignmentRecord":
"""Extract information from a pysam Aligned segment"""
read_name, read_idx, align_idx = align.query_name.split(":")
read_idx, align_idx = int(read_idx), int(align_idx)
if align.is_unmapped:
align_cat = "unmapped"
chrom, start, end, align_score = "NULL", 0, 0, 0
read_length = align.query_length
quals = align.query_qualities
# TODO: handle this more gracefully
if quals is None:
align_base_qscore = 0
else:
align_base_qscore = mean_qscore(np.array(
align.query_qualities))
else:
chrom, start, end = (align.reference_name, align.reference_start,
align.reference_end)
read_length = align.infer_read_length()
align_score = align.get_tag("AS")
align_base_qscore = mean_qscore(
np.array(align.query_alignment_qualities))
if align.is_secondary:
align_cat = "secondary"
elif align.is_supplementary:
align_cat = "supplementary"
else:
align_cat = "primary"
optional = {}
for key, tag in [("haplotype", "HP"), ("phase_set", "PS"),
("phase_qual", "PC")]:
if align.has_tag(tag):
optional[key] = int(align.get_tag(tag))
return cls(
read_idx=read_idx,
align_idx=align_idx,
align_type=align_cat,
chrom=chrom,
start=start,
end=end,
strand=not align.is_reverse,
read_name=read_name,
read_length=read_length,
read_start=align.query_alignment_start,
read_end=align.query_alignment_end,
mapping_quality=align.mapq,
align_score=align_score,
align_base_qscore=np.rint(align_base_qscore),
**optional,
)
def get_qc_fail(rec: pysam.AlignedSegment) -> Optional[Tuple[str, str]]:
"""Gets the tool and reason for why the QC fail flag is set, otherwise None if not set.
If the QC fail flag is set, but the tool and filter reason SAM tags are not set, None will be
returned. Use pysam.AlignedSegment.is_qcfail() to check if the record is simply QC failed.
Args:
rec: the record to fail
"""
if not rec.is_qcfail or not rec.has_tag(QcFailToolTag):
return None
else:
tool_value = rec.get_tag(QcFailToolTag)
reason_value = rec.get_tag(QcFailReasonTag)
return (tool_value, reason_value)